Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1680 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0123570452 sf0123569408 1 23570452 7.26E-07 7.26E-07
vg1220148590 sf1220120032 12 20148590 2.27E-06 2.27E-06
vg0818761789 sf0818759076 8 18761789 3.61E-06 3.61E-06
vg0421045958 sf0420874012 4 21045958 3.97E-06 3.97E-06
vg0420801865 sf0420629908 4 20801865 4.34E-06 4.34E-06
vg0813739257 sf0813736543 8 13739257 4.37E-06 4.37E-06